| Variant ID: vg0403670419 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3670419 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, G: 0.05, others allele: 0.00, population size: 74. )
CCAGCATCAGGCGAGGCCACACACGCTCCTCGTGCACGACCAGCCCGCAGAGCGCGTCCTGGCACGGCGCGTTCTGCACCGCCTCTGTCACAGCGAGCAA[C/G]
AAAGCTGGGCCAGCATCCTCAGTTTGCGCAAGATGAGCTTCAGCCTTCTTCTTCTTGGGGTGTGGACACTGCGTGGAGTAGTGGCCAAACTCCTCACAGT
ACTGTGAGGAGTTTGGCCACTACTCCACGCAGTGTCCACACCCCAAGAAGAAGAAGGCTGAAGCTCATCTTGCGCAAACTGAGGATGCTGGCCCAGCTTT[G/C]
TTGCTCGCTGTGACAGAGGCGGTGCAGAACGCGCCGTGCCAGGACGCGCTCTGCGGGCTGGTCGTGCACGAGGAGCGTGTGTGGCCTCGCCTGATGCTGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.60% | 24.70% | 1.23% | 19.47% | NA |
| All Indica | 2759 | 62.70% | 30.80% | 1.38% | 5.07% | NA |
| All Japonica | 1512 | 43.60% | 6.80% | 0.73% | 48.88% | NA |
| Aus | 269 | 50.60% | 40.90% | 1.86% | 6.69% | NA |
| Indica I | 595 | 95.10% | 4.20% | 0.17% | 0.50% | NA |
| Indica II | 465 | 68.00% | 28.00% | 0.65% | 3.44% | NA |
| Indica III | 913 | 40.60% | 49.20% | 2.74% | 7.45% | NA |
| Indica Intermediate | 786 | 60.80% | 31.30% | 1.15% | 6.74% | NA |
| Temperate Japonica | 767 | 50.10% | 0.30% | 0.26% | 49.41% | NA |
| Tropical Japonica | 504 | 24.20% | 18.10% | 1.39% | 56.35% | NA |
| Japonica Intermediate | 241 | 63.50% | 4.10% | 0.83% | 31.54% | NA |
| VI/Aromatic | 96 | 10.40% | 80.20% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 51.10% | 28.90% | 3.33% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403670419 | C -> DEL | LOC_Os04g06960.1 | N | frameshift_variant | Average:28.192; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | N | N | N | N |
| vg0403670419 | C -> G | LOC_Os04g06960.1 | missense_variant ; p.Leu130Phe; MODERATE | nonsynonymous_codon ; L130F | Average:28.192; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | unknown | unknown | DELETERIOUS | 0.01 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403670419 | 3.27E-07 | 5.78E-08 | mr1227 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0403670419 | NA | 7.72E-09 | mr1570 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0403670419 | NA | 4.40E-06 | mr1540_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0403670419 | NA | 2.71E-07 | mr1558_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |